The # of total users on the Mac Mini is not good, not just the # of remote clients... Make sure to turn the stats.log and top call stats log on. Unless the solution is extremely light I wouldn't expect that box to hold up well. Those logs will give you some solid numbers on that.

The remote clients are also running FM16 now?

Did you remove/rename the leftover "filemaker server" folder from /Library after uninstalling FMS14?

wimdecorte is right about the number of users on a mac mini server that in itself is impressive. is comments and questions are valid but I would expect that it would be slower because a significant number of events are now being handled by the server rather than the clients so is it faster and less "noisy" on the network but with that number of users it will be maxing out